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Vasant Marur
Versatile Bioinformatician and Data Scientist with 15+ years’ experience deriving insights from mutlidimensional data using statistical and machine learning methods. My recent work focuses on analysis of sleep study data to find lipidomic biomarkers that are circadian, and entails a hands-on approach through the full data lifecycle from raw instrument data collection to munging, analysis, visualization and results write-up. Core skill sets:
- Hypothesis testing methods and regression models
- Machine learning for dimension reduction, clustering, and applying classification & prediction algorithms
- Publication-quality data visualizations using ggplot and ploty for interactive plots and proficient in building apps in R/Shiny
- Finding, assessing, and applying new tools and techniques to address specialized data or research study requirements
- Managing core system and process elements of an applied bioinformatics lab, including database and web server administration, creation of data shares and pipelines, instrument interface development and configuration, and general data management
- Applying my analytical expertise in an inter-disciplinary environment that requires both guiding and learning from my collaborators
Experience
Research Specialist
Div. of Sleep & Circadian Disorders, Brigham & Women’s Hospital
Boston, MA
Current - Jan 2016
Focus: Identifying circadian lipidomic biomarkers to link sleep restriction to diabetes, and cardiovascular risk, and to report circadian phase and alignment
- Translated existing SAS code for cosinor models to R, and applied other field specifc specialized algorithms to find rhythmicity and compare results with cosinor methods
- Wrote reusable analytic pipeline in R for using above algorithms to find Circadian Rhythms in numerous lipidomic datasets relating to sleep studies under different conditions with collaborators
- Built and maintained lipidomics pipeline - Automated the identification of lipids from mass spec data using in-house curated database, significantly reducing time and manual effort required from researchers
- Evaluated and configured software for quantitation of mass spec data. Established overall Data Management process and SOPs for creating and sharing data with collaborators
- Manage a mix of Windows servers for High Performance Computing, Linux Servers for hosting databases, and webservers (nginx) for hosting apps built with R/Shiny and Python/Flask
Research Specialist
Dept. of Neurosurgery, Brigham & Women’s Hospital
Boston, MA
Jan 2016 - Apr 2007
Focus: Linking metabolomic and proteomic profiles to risk of future disease – specifically breast cancer and Type II Diabetes.
- Applied statistical and informatics analysis to large experimental clinical studies
- Analyzed mass spec data relating proteomic profiles to understand effects of Calorie Restriction on longevity as part of the CALERIE trial
- Used informatics analysis to assess impacts of specimen quality and integrity on the identification of biomarkers
- Created data shares, built data pipelines, and managed onsite and remote backups of personnel and instrument data
Senior Research Assitant III
Burke Medical Research Institute
White Plains, NY
Apr 2007 - Sep 2005
- Performed informatics analysis of metabolomic profiles from Dietary restriction studies in order to identify biomarkers predicting the risk of Type II Diabetes
- Used ML & statistical approaches to determine predictors of rehabilitation outcomes for patients with traumatic brain injuries
- Interfaced lab instruments with computers for data collection and recovery
Graduate Research Assistant
Bioinformatics Lab, Marquette University
Milwaukee, WI
May 2005 - Sep 2004
- Masters’ Thesis: Developed a software system to curate bio-medical literature, including automated data collection and management, application of ML algorithms to find and rank relevant literature, and development of a web interface to display results
- System Administration: Managed user accounts, performed troubleshooting, system backups and database setup for Windows and Unix/Linux operating systems and servers, and configured new Bioinformatics analysis software
Education
MS Bioinformatics
Marquette University & Medical College of Wisconsin
Milwaukee,WI
2005 - 2003
- Thesis: An SVM based tool for the curation of biomedical literature
Post Grad. Diploma in Information Technology
University of Mumbai
Mumbai,India
2003 - 2002
B.Sc. Statistics & Operations Research
Ramnarain Ruia College, University of Mumbai
Mumbai,India
2002 - 1999